Stone-throwing Muslim men battled Kenyan security forces armed with tear gas and rubber bullets in the coastal city of Mombasa for a second day on Monday, after two protesters and a police officer died during unrest at the weekend.

Roads were blocked, shops attacked and cars trashed as hundreds of young men gathered close to a central Mombasa mosque where preachers are accused of promoting violent radicalism.

Associates of Samantha Lewthwaite, the British Muslim convert and widow of a July 7 bomber, who Kenya is seeking in connection to terror charges, were known to worship at the Musa mosque.

Police raided the property on Sunday after officers raised suspicions that meetings were being held to radicalise disaffected young Muslims.

More than 125 people were arrested in the ensuing clashes. All will be charged with “being members of a terrorist group, namely al-Shabaab” in the coming days, police said on Monday.

al-Shabaab is a jihadist al-Qaeda franchise based in Somalia, but also active in Kenya.

“They were all over the streets, blocking cars, if you did not stop they threw stones at your vehicle,” said Abdul Ali Karim, a mechanic in the city.

“There is good reason for anger. They are being poorly treated by the police. But there is still no reason to block the town and stop our businesses.”

Muslim human rights groups have repeatedly accused the Kenyan Police of heavy-handed tactics in their pursuit of alleged terror suspects or sympathisers of al-Shabaab.

Dozens, possibly hundreds, of young Kenyan Muslims have crossed the border to Somalia to train there with al-Shabaab forces. It is feared that many have since crossed back into Kenya where they are planning fresh attacks.

More than 70 people died when a four-man al-Shabaab cell took over the Westgate shopping centre in the capital, Nairobi, and besieged it for four days before they were killed.

There were a series of urgent warnings of possible fresh incidents over the weekend. Security at shopping centres has been increased, and checks on passengers and vehicles entering all of Kenya’s airports have been boosted.